We recently reported that biomedical researchers should be aware of genetic and phenotypic differences in C57BL/6 substrains. This knowledge is particularly important when doing studies with genetically engineered mice (GEM) on a C57BL/6 background. Mispairing of GEM with the wrong C57BL/6 substrain control can lead to erroneous and misleading findings as we found recently studying the pathological role of c-Jun N-terminal kinase 2 in acetaminophen- and concanavalin A -induced liver injury. Recent unbiased genome-wide expression analyses with exon array and RNA-SEQ technologies of liver homogenates from acetaminophen-treated C57BL/6J mice from the Jackson Laboratory and C57BL/6NTac mice from Taconic Farms revealed numerous differences in expressed genes, spliced variants, and signal nucleotide variations between the two substrains of C57BL/6 mice. Many of these genetic events were confirmed at the protein level. Conclusion: It is anticipated that further studies and analyses of our genetic expression data will uncover risk factors that may play roles in determining susceptibility of patients to drug-induced liver injury.